Ask Stalin about his efforts to eradicate religion...
Mao on his cultural necessity
Or Hitler on his final solution...
Hitler wasn't really an atheist, but let's run with the idea that he was if you like.
We might ask the following question: did these people order mass killings etc.
because of atheism? Were the killings carried out in the name of atheism? Were they carried out primarily to advance the cause of atheism?
The answers to those questions are fairly obvious, don't you think? If not, let me provide them for you: no and no and no.
Autocrats tend to dislike religions because they diminish the power of the State (i.e. the Autocrat and his cronies). The best thing that an autocrat can do is to create a new kind of religion that has the State itself, or the Great Leader, as the object of veneration, rather than a traditional god or gods. If you doubt this, witness the monuments that the autocrats create to themselves - the giant statues, their faces on every billboard, the portrait hung compulsorily in every office (and, preferably, every home). The autocrat will denounce traditional religion as an evil, and might use atheism as an excuse to purge the power of religion, but the end goal is not to obliterate religion. Rather it is to replace existing religion with a religion controlled and dictated by the autocrat. If the Autocrat can get himself to the point of being considered as a deity or demi-god, all the better for him.
Autocrats kill people for political reasons, and for ideological reasons. None of them kill to advance atheism as some kind of "pure" philosophy.